That's early for coolant pump failure, but that happens a lot to these cars. Now the leak on the gearbox is more unusual. Is it CPO ? There is a possibility that the head gasket leaks after pump failure, better knowing you have recourse if its the case.
The rest is usual stuff for a N54 (recalls on HPD, etc). So its not much to worry about, actually its a sign you got the upgraded parts that work better. The column thing is probably replaced because it had a tendency to rattle on many cars.